Bin Chen CV

Bin Chen

**** ***** ***** ******, ***********, IN 47403

abpa30@r.postjobfree.com 812-***-****

http://cheminfo.informatics.indiana.edu/~binchen/

OBJECTIVES

Obtain a position where I can maximize my skills in cheminformatics, bioinformatics,

semantic web and statistical learning.

EDUCATION

2009-2012 Indiana University, Bloomington, IN

(expected) Ph.D., Informatics, GPA: 3.9/4.0

Minor: Cheminformatics and Bioinformatics

Thesis: Towards semantic systems chemical biology

Advisor: Prof. David Wild

2007-2009 Indiana University, Bloomington, IN

M.S., Cheminformatics

2000-2004 Chongqing University, China

B.S., Chemistry

PROFESSIONAL EXPERIENCE

2/2012-present Semantic Web developer at Novartis Institutes of Biomedical Research,

Boston, MA

8/2007-1/2012 Research Assistant under Prof. David Wild at School of Informatics and

Computing, Indiana University at Bloomington

6/2011-8/2011 Intern under Dr. Robert Sheridan at Merck, Rahway, NJ

6/2010-8/2010 Intern under Dr. Eric Gifford at Pfizer Global Research & Development,

Groton, CT

6/2009-8/2009 Intern under Dr. Eric Gifford at Pfizer Global Research & Development,

Groton, CT

6/2008-8/2008 Intern under Dr. Josef Scheiber at Novartis Institutes of Biomedical

Research, Boston, MA

7/2004-7/2007 Research Assistant under Prof. Weiming Chen at Shanghai Institute of

Organic Chemistry, Chinese Academy of Sciences

RESEARCH ACHEIVEMENTS

Semantic Web technologies in Systems Chemical Biology

2009-2011 Chem2Bio2RDF: a semantic framework for systems chemical biology

(with Ying Ding and David Wild)

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Bin Chen CV

Created a RDF-based resource by aggregating data from over 20 public

sources pertaining to Drugs, Chemical Compounds, Protein Targets, Diseases,

Side Effects and Pathways. Applied the linked data in investigating

polypharmacology, multiple pathway inhibition and adverse drug reaction -

pathway mapping. The paper has been cited over 30 times since published in

2010 and its website has been visited over 30,000 times.

2010-2011 Chem2Bio2OWL: a Web Ontology for systems chemical biology and

chemogenomics (with Ying Ding and David Wild)

Developed web ontology to annotate Chem2Bio2RDF data, making it a rich

semantic resource, simplifying the process of SPARQL construction and making

possible intelligent reasoning.

2010-2011 SLAP: a novel algorithm for drug target prediction using semantic

linked data (with Ying Ding and David Wild)

Developed a statistical model called SLAP (Semantic Linked Association

Prediction) to assess the association of drug target pairs based on their

relation with other linked objects (borrowed the idea from social network) in a

large semantic linked network. Partnered with medicinal chemists to

investigate its use in identifying novel PXR antagonists and TB inhibitors.

Developed SLAP as a deliverable product (chem2bio2rdf.org/slap) to facilitate

open drug target identification and drug repurposing. Various validation

experiments show it can achieve a high level of precision.

Network Polypharmacology

2011-present Relating drugs using biological fingerprints (with David Wild)

Assessed drugs similarity using biological fingerprints composed by the SLAP

results against hundreds of targets. The established similarity network indicates

that drugs from the same disease area tend to cluster together in ways which

are not captured by structural similarity, with several potential new drug

pairings being identified.

2010 summer Comparing Bioassay Response and Similarity Ensemble Approach

(SEA) to probing protein pharmacology (with Nikil Wale, Kevin

McConnell and Eric Gifford)

Created protein networks based on ligand similarity (SEA) and ligand bioassay

response-data (BARD) using 155 Pfizer internal BioPrint assays. Exploited

various statistical association methods including Spearman's rank correlation

coefficient, Tanimoto coefficient, Wilcoxon signed rank test and

Polypharmacology interaction strength. Demonstrated both approaches can be

used complementarily.

2008-2009 Building a polypharmacology network using PubChem BioAssay data

(with Rajarshi Guha)

Developed a network representation of assay collections and then applied a

bipartite mapping between this network and various biological networks (i.e.,

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Bin Chen CV

PPI, pathway) as well as artificial networks (i.e., drug-target network).

Mapping results could help prioritize new selective compounds and validate

target pairs.

2008 summer Investigating off-target mediated effects of drug candidates using

systems chemical biology approach (with Josef Scheiber and other

scientists in lead informatics discovery group at Novartis)

Developed a workflow that leverages data from chemogenomics based target

predictions with Systems Biology databases (e.g., Pathway, PPI) to better

understand off-target related toxicities. Linked pathways and adverse drug

reactions and found evidences in literature. Investigated a particular adverse

drug reaction in the early toxicity group.

QSAR modeling

2011 summer Comparing Na ve Bayesian with Random Forest systematically (with

Robert Sheridan, Johannes Voigt and Viktor Hornak)

Wrapped Na ve Bayesian in Pipeline Pilot (PLPNB) as a UNIX based tool.

Compared the ability of PLPNB and Random Forest (RF) to make simulated

prospective predictions on 18 Merck in-house QSAR datasets including

on-target and ADME-related activities. Results showed that PLPNB is efficient

while RF overall outperform PLPNB in terms of accuracy.

2009 summer Characterizing molecular similarity ADME landscapes (with Rishi

Gupta and Eric Gifford)

Applied various molecular similarity methods to characterize chemical

landscapes for 9 ADME (Absorption, Distribution, Metabolism, and Excretion)

endpoints. Results show that landscapes behave differently among endpoints

and the observation can be quantified to prioritize compounds while

transforming compound from HIGH risk class to LOW risk class.

2007-2008 Modeling PubChem BioAssay using Na ve Bayesian (with David Wild)

Investigated the quality of naive Bayesian predictive models built using

PubChem BioAssay data. Found that overall the predictive quality of such

models is good, indicating that they could have utility in virtual screening.

Miscellaneous

2010-2011 Building web service based predictive models using various approaches

including SLAP, SEA, Na ve Bayesian and occurrences in literature.

(with Qian Zhu and David Wild)

2011 spring Characterizing the distance of drug targets in a protein pharmacology

network (individual work)

2011 spring Exploring protein pharmacology network threshold selection and

modeling the network using exponential random graph models

(Network Science course work)

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Bin Chen CV

2010 fall Assessing protein relations using dimension reduction methods

including PCA, CMDS and ISOMAP (Data Mining course work)

2010 Visualizing large scale cheminformatics data with dimension reduction

(with High Performance Computing group)

2009 spring Using network techniques to mine scientific abstracts relating to

chemistry (Web mining course work)

2008 spring Finding binding sites of Falcipain-2 using blind docking (Structural

Bioinformatics course work)

Identifying validated molecular transformations in PubChem for lead

2008

design (with Abbott laboratories)

2004-2007 Developed and maintained Abstracts Processing System for Chemical

Abstracts Services (CAS), Chinese Journal Processing System, Reaction

Processing System for CASReact and Compound Name Translation

System (with Weiming Chen)

TECHNICAL SKILLS

Languages: JAVA, R, Python, VB/VBA, RDF/OWL, Perl

Databases: SQL, MS Access, Postgres, Virtuoso

Web development: HTML, XML, ASP, Ajax, Web Service, RESTful service

Miscellaneous: Pipeline Pilot, AUTODOCK, Spotfire

SERVICES and ACADEMIC ACTIVITIES

Program Committee for

o International Workshop on Semantic Technologies for information Integrated

Collaboration (STIIC 2010)

o 10th International Workshop on Data Mining in Bioinformatics(BIOKDD

2011)

o International Workshop on Semantic Technologies for information Integrated

Collaboration (STIIC 2011)

o First international workshop on Knowledge Discovery and Data Mining

Meets Linked Open Data (Know@LOD) co-located with ESWC 2012

o 11th International Workshop on Web Semantics and Information Processing

(WebS 2012)

o International Workshop on Semantic Technologies for information Integrated

Collaboration (STIIC 2012)

o Special Issue on Mining Associations and Patterns from the Semantic Data

(2012)

o 3rd International Conference on Innovations in Bio-Inspired Computing and

Applications (IBICA-2012)

o Mining Data Semantics in Information Networks Workshop (MDS 2012) in

conjunction with SIGKDD 2012

Reviewer for Journal of Cheminformatics, IEEE intelligent systems, Journal of

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Bin Chen CV

Chemical Information and Modeling, Journal of Information Science, Knowledge and

Information Systems, Social Network Analysis and Mining, Journal of Biomedical

Semantics

Mentor for thesis projects for several graduate students

Teaching assistant (volunteered) for Semantic Web course taught by Ying Ding (2011

spring and fall)

Organizer for Cheminformatics Journal Club at Indiana University

AWARDS

$30,000 Symyx Ph.D. Fellowship 2009

$1,000 CINF Scholarship for Scientific Excellence 2010 (including presentation at an

ACS national meeting)

First place in poster competition, Center for Bioinformatics Research Industry

Collaboration Workshop on Life Sciences Informatics, May 2010

Conference on Semantic in Healthcare and Life Science (CSHALS 2012) student

travel fellowship

$1,500 Lucille Wert Scholarship 2012 (ACS Chemical Information Division)

JOURNAL PUBLICATIONS

Bin Chen, Ying Ding, David Wild, Drug target prediction using semantic linked data

(under review)

Bin Chen, Robert Sheridan, Johannes Voigt and Viktor Hornak, Comparing Na ve

Bayesian in Pipeline Pilot with Random Forest in QSAR modeling, J Chem Inf

Model., 2012, 52(3):792-803

Bin Chen, Ying Ding, David Wild, Improving integrative searching of Systems

Chemical Biology data using semantic annotation, Journal of Cheminformatics, 2012,

4(1):6

He, B., Tang, J., Ding, Y., Wang, H., Sun, Y., Shin, J.H., Chen, B., Moorthy, G., Qiu,

J., Desai, P., Wild, D.J., Mining relational paths in biomedical data, PLOS, 2011,

e27506

Chen B, McConnell KJ, Wale N, Wild DJ, Gifford EM. Comparing Bioassay

Response and Similarity Ensemble Approaches to Probing Protein Pharmacology,

Bioinformatics, 2011, 27(21):3044-9

Choi, J.Y., Bae, S.H., Qui, J., Chen, B., Wild, D.J. Browsing large scale

cheminformatics data with dimension reduction. Currency and Computation: Practice

and Experience, 2011

Chen, B., Dong. X., Jiao, D., Wang, H., Zhu, Q., Ding, Y., Wild, D.J.

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic

and systems chemical biology data. BMC Bioinformatics, 2010, 11:255

Chen B, Wild D. PubChem as a data source for predictive models, J Mol Graph

Model., 2010, 28(5):420-6

Chen B, Wild D, Guha R. PubChem Bioassays as a Source of Polypharmacology, J

Chem Inf Model., 2009, 49(9), 2044-55

Scheiber J, Chen B, Milik M, Sukuru SC, Bender A, Mikhailov D, Whitebread S,

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Bin Chen CV

Hamon J, Azzaoui K, Urban L, Glick M, Davies JW, Jenkins JL. A Comprehensive

Systems Chemical Biology Analysis Gains Insight into Off-Target Mediated Effects

of Drug Candidates, J Chem Inf Model., 2009, 49 (2), 308 317

CONFERENCE PUBLICATIONS

Choi, J.Y., Bae, S.H., Qiu, J., Fox, G., Chen, B., Wild. D.J. Browsing Large Scale

Cheminformatics Data with Dimension Reduction. Emerging Computational Methods

for the Life Sciences Workshop, ACM Symposium for High Performance Distributed

Computing Jun 21-25, 2010, Chicago, IL

Ding, Y., Sun, Y., Chen, B., Borner, K., Ding, L., Wild, D., Wu, M., DiFranzo, D.,

Fuenzalida, A. G., Li, D., Milojevic, S., Chen, S., Sankaranarayanan, M. & Toma, I.

Semantic Web Portal: A Platform for Better Browsing and Visualizing Semantic Data.

/Proceedings of the 2010 International Conference On Active Media Technology

(AMT2010), Lecture Notes in Artificial Intelligence (LNAI), /Springer, Aug 28-30,

Toronto, Canada

Chen, B., Ding, Y., Wang, H., Wild, D., Dong, X., Sun, Y., Zhu, Q., &

Sankaranarayanan, M. (2010). Chem2Bio2RDF: A Linked Open Data Portal for

Chemical Biology. 2010 /IEEE/WIC/ACM International Conferences on Web

Intelligence/, Aug 31 Sep 3, 2010, Toronto, Canada (Regular Paper, accept rate

16.6%, Best paper shortlist)

Dong, X., Ding, Y., Wang, H., Chen, B., Wild, D.J. Chem2Bio2RDF Dashboard:

Ranking Semantic Associations in Systems Chemical Biology Space. Future of the

Web in Collaboratice Science (FWCS), WWW2010, Apr 26-30, 2010, Raleigh NC

PRESENTATIONS

Bin Chen, Ying Ding, David Wild, Beyond Semantic Integration: Drug Target

Prediction using Semantic Linked Data, poster at Bio-IT 2012, Boston, MA, April.

2012

Bin Chen, Ying Ding, David Wild, Assessing Drug Target Association using Semantic

Linked Data, Conference on Semantics in Healthcare and Life Sciences 2012,

Cambridge, MA, Feb. 2012

Bin Chen, Ying Ding, Huijun Wang, Bing He, Xiao Dong, Qian Zhu, Jie Tang, Philip

Yu, Eric Gifford, David Wild, Semantic Systems Chemical Biology: from data

annotation and integration to data mining, poster at Conference on Semantics in

Healthcare and Life Sciences 2012, Cambridge, MA, Feb. 2012

Bin Chen, Ying Ding, David Wild, Drug Target Prediction using Semantic Linked

Data, Poster at Inaugural Conference of the International Chemical Biology Society,

Kansas City, MO, Oct. 2011

Bin Chen, Rishi Gupta, Eric Gifford, Molecular similarity characterization of ADME

landscapes, 239th ACS National Meeting, San Francisco, CA, Mar. 2010

Bin Chen, Ying Ding, David Wild, Chem2Bio2RDF: Semantic Systems Chemical

Biology, 239th ACS National Meeting, San Francisco, CA, Mar. 2010(Best Poster

Award)

Bin Chen, David Wild and Rajarshi Guha, PubChem Bioassays as a Source of

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Bin Chen CV

Polypharmacology, 236th ACS National Meeting, Philadelphia, PA, Aug. 2008

INVITED TALKS

Drug target prediction using semantic linked data, Mayo Clinic, Rochester, MN, Nov.

2011

From data integration to data mining in Semantic Web, Lecture for S636, Indiana

University at Bloomington, Nov. 2011

Towards Semantic Systems Chemical Biology, Knowledge transfer seminar at Merck

Inc., Rahway, NJ, Jul. 2011

Building a web ontology for systems chemical biology, Lecture for S604, Indiana

University at Bloomington, Apr. 2011

Overview of Chem2Bio2RDF, Seminar at Pfizer Inc., Boston, MA, Aug. 2010

Chem2Bio2RDF: Semantic Systems Chemical Biology, Seminar at Kno.E.SIS,

Wright State University, Nov. 2009

REFERENCES

Available upon request

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